Strong Binding Affinity of a Zinc-Porphyrin-Based Receptor for Halides through the Cooperative Effects of Quadruple CH Hydrogen Bonds and Axial Ligation

2011 ◽  
Vol 17 (49) ◽  
pp. 13898-13903 ◽  
Author(s):  
Chi-Hwa Lee ◽  
Sangeun Lee ◽  
Hongsik Yoon ◽  
Woo-Dong Jang
Keyword(s):  
Hydrogen Bonds ◽  
Binding Affinity ◽  
Zinc Porphyrin ◽  
Cooperative Effects ◽  
Axial Ligation ◽  
Strong Binding

scholarly journals Design of peptides with strong binding affinity to poly(methyl methacrylate) resin by use of molecular simulation-based materials informatics

2021 ◽  
Author(s):  
Tomio Iwasaki ◽  
Masashi Maruyama ◽  
Tatsuya Niwa ◽  
Toshiki Sawada ◽  
Takeshi Serizawa
Keyword(s):  
Methyl Methacrylate ◽  
Binding Affinity ◽  
Molecular Simulation ◽  
Dynamics Simulation ◽  
Binding Affinities ◽  
Materials Informatics ◽  
Poly Methyl Methacrylate ◽  
Strong Binding ◽  
Experimental Values ◽  
Pmma Resin

AbstractPeptides with strong binding affinities for poly(methyl methacrylate) (PMMA) resin were designed by use of materials informatics technology based on molecular dynamics simulation for the purpose of covering the resin surface with adhesive peptides, which were expected to result in eco-friendly and biocompatible biomaterials. From the results of binding affinity obtained with this molecular simulation, it was confirmed that experimental values could be predicted with errors <10%. By analyzing the simulation data with the response-surface method, we found that three peptides (RWWRPWW, EWWRPWR, and RWWRPWR), which consist of arginine (R), tryptophan (W), and proline (P), have strong binding affinity to the PMMA resin. These amino acids were effective because arginine and tryptophan have strong binding affinities for methoxycarbonyl groups and methyl groups, which are the main constituents of the PMMA resin, and proline stabilizes the flat zigzag structures of the peptides in water. The strong binding affinities of the three peptides were confirmed by experiments (surface plasmon resonance methods).

scholarly journals Epitope-Based Peptide Vaccine Against Fructose-Bisphosphate Aldolase of Madurella mycetomatis Using Immunoinformatics Approaches

2018 ◽  
Vol 12 ◽  
pp. 117793221880970 ◽  
Author(s):  
Arwa A Mohammed ◽  
Ayman MH ALnaby ◽  
Solima M Sabeel ◽  
Fagr M AbdElmarouf ◽  
Amina I Dirar ◽  
...  
Keyword(s):  
B Cell ◽  
Binding Affinity ◽  
Mhc Class Ii ◽  
Bacterial Infections ◽  
Peptide Vaccine ◽  
Fructose Bisphosphate ◽  
Mhc I ◽  
Strong Binding ◽  
Fructose Bisphosphate Aldolase ◽  
Madurella Mycetomatis

Background: Mycetoma is a distinct body tissue destructive and neglected tropical disease. It is endemic in many tropical and subtropical countries. Mycetoma is caused by bacterial infections ( actinomycetoma) such as Streptomyces somaliensis and Nocardiae or true fungi ( eumycetoma) such as Madurella mycetomatis. To date, treatments fail to cure the infection and the available marketed drugs are expensive and toxic upon prolonged usage. Moreover, no vaccine was prepared yet against mycetoma. Aim: The aim of this study is to predict effective epitope-based vaccine against fructose-bisphosphate aldolase enzymes of M. mycetomatis using immunoinformatics approaches. Methods and materials: Fructose-bisphosphate aldolase of M. mycetomatis sequence was retrieved from NCBI. Different prediction tools were used to analyze the nominee’s epitopes in Immune Epitope Database for B-cell, T-cell MHC class II and class I. Then the proposed peptides were docked using Autodock 4.0 software program. Results and conclusions: The proposed and promising peptides KYLQ show a potent binding affinity to B-cell, FEYARKHAF with a very strong binding affinity to MHC I alleles and FFKEHGVPL that shows a very strong binding affinity to MHC II and MHC I alleles. This indicates a strong potential to formulate a new vaccine, especially with the peptide FFKEHGVPL which is likely to be the first proposed epitope-based vaccine against fructose-bisphosphate aldolase of M. mycetomatis. This study recommends an in vivo assessment for the most promising peptides especially FFKEHGVPL.

Supramolecular self-assemblies of inverted cucurbit[7]uril with biogenic amines

2019 ◽  
Vol 43 (1) ◽  
pp. 407-412
Author(s):  
Pei-Hui Shan ◽  
Zhi-Rui Zhang ◽  
Dong Bai ◽  
Bing Bian ◽  
Zhu Tao ◽  
...  
Keyword(s):  
Biogenic Amines ◽  
Binding Affinity ◽  
Biogenic Amine ◽  
Binding Sites ◽  
Experimental Results ◽  
Binding Interactions ◽  
Strong Binding

The binding interactions between six biogenic amine guests and the iQ[7] host were investigated. The experimental results have revealed that iQ[7] shows strong binding affinity towards five of the studied biogenic amines, but not histamine, and that the binding sites are different depending on the structure of the biogenic amine.

The remarkable activity and stability of a dye-sensitized single molecular layer MoS2ensemble for photocatalytic hydrogen production

2015 ◽  
Vol 51 (70) ◽  
pp. 13496-13499 ◽  
Author(s):  
Tiantian Jia ◽  
Molly M. J. Li ◽  
Lin Ye ◽  
Sam Wiseman ◽  
Guoliang Liu ◽  
...  
Keyword(s):  
Hydrogen Production ◽  
Binding Affinity ◽  
Molecular Layer ◽  
Single Layer ◽  
Eosin Y ◽  
Photocatalytic Hydrogen Production ◽  
Dye Sensitized ◽  
Strong Binding ◽  
Single Molecular Layer ◽  
Dye Molecule

Single layer MoS2synthesized by exfoliation with Li is demonstrated to take up the dye molecule, Eosin Y, with strong binding affinityviasulfur vacancies.

Abstract 5790: TG-1601 is a novel BET inhibitor with strong binding affinity and long-lasting effect in pre-clinical models

2018 ◽  
Author(s):  
Emmanuel Normant ◽  
Leonid Gorelik ◽  
Rama Shmeis ◽  
Henry Le ◽  
Robert Nisch ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Bet Inhibitor ◽  
Lasting Effect ◽  
Strong Binding ◽  
Clinical Models

scholarly journals A 2,3-dialkoxynaphthalene-based naphthocage

2020 ◽  
Vol 56 (6) ◽  
pp. 888-891 ◽  
Author(s):  
Song-Bo Lu ◽  
Hongxin Chai ◽  
Jas S. Ward ◽  
Mao Quan ◽  
Jin Zhang ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Organic Cations ◽  
Strong Binding

A 2,3-dialkoxynaphthalene-based naphthocage was synthesized. It shows similarly strong binding affinity to organic cations as the 2,6-dialkoxynaphthalene-based naphthocage but different guest preference and conformational response.

scholarly journals Docking of Platinum Compounds on Cube Rhombellane Functionalized Homeomorphs

Symmetry ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 749
Author(s):  
Beata Szefler ◽  
Przemysław Czeleń
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Binding Affinity ◽  
Fullerene C60 ◽  
C60 Fullerene ◽  
Binding Affinities ◽  
Hydrogen Bond Network ◽  
Platinum Compounds ◽  
Anti Cancer ◽  
Bond Network

Platinum compounds are anti-cancer drugs and can bind to canonical purine bases, mainly guanine, found within double helical DNA. Platinum compounds can be transferred directly to pathologically altered sites in a specific and site-oriented manner by nanocarriers as potential nanocarriers for carboplatin. Two types of nanostructures were used as potential nanocarriers for carboplatin, the first were functionalized C60 fullerene molecules and the second were rhombellanes. The analyzed nanostructures show considerable symmetry, which affects the affinity of the studied nanocarriers and ligands. Thus symmetry of nanostructures affects the distribution of binding groups on their surface. After the docking procedure, analysis of structural properties revealed many interesting features. In all described cases, binding affinities of complexes of platinum compounds with functionalized fullerene C60 are higher compared with affinities of complexes of platinum compounds with rhombellane structures. All platinum compounds easily create complexes with functionalized fullerene C60, CID_16156307, and at the same time show the highest binding affinity. The binding affinities of lobaplatin and heptaplatin are higher compared with oxaliplatin and nedaplatin. The high value of binding affinity and equilibrium constant K is correlated with creation of strong and medium hydrogen bonds or is correlated with forming a hydrogen bond network. The performed investigations enabled finding nanocarriers for lobaplatin, heptaplatin, oxaliplatin and nedaplatin molecules.

Sign in / Sign up

Export Citation Format

Share Document